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3D SIM

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https://www.readbyqxmd.com/read/28192239/super-silac-mix-coupled-with-sim-aims-assays-for-targeted-verification-of-phosphopeptides-discovered-in-a-large-scale-phosphoproteome-analysis-of-hepatocellular-carcinoma
#1
Yu-Tsun Lin, Kun-Yi Chien, Chia-Chun Wu, Wen-Yu Chang, Lichieh Julie Chu, Min-Chi Chen, Chau-Ting Yeh, Jau-Song Yu
: Plentiful studies have established a close association between aberrant phosphorylation and hepatocellular carcinoma (HCC). Here, we applied a quantitative phosphoproteomics platform combining dimethylation labeling and online 3D strong cation exchange chromatography (SCX)-titanium oxide (TiO2)/RP-LTQ-Orbitrap to compare phosphoproteomes between three pairs of HCC tissues and non-tumor counterparts. This analysis yielded 7868 quantifiable phosphopeptides and numerous up- or down-regulated candidates...
February 10, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28155594/pbpk-modeling-a-predictive-eco-friendly-bio-waiver-tool-for-drug-research
#2
Baishakhi De, Koushik Bhandari, Ranjan Mukherjee, Prakash Katakam, Shanta K Adiki, Rohit Gundamaraju, Analava Mitra
BACKGROUND: The world has witnessed growing complexities in disease scenario influenced by the drastic changes in host-pathogen- environment triadic relation. Pharmaceutical R&Ds are in constant search of novel therapeutic entities to hasten transition of drug molecules from lab bench to patient bedside. Extensive animal studies and human pharmacokinetics are still the "gold standard" in investigational new drug research and bio-equivalency studies. Apart from cost, time and ethical issues on animal experimentation, burning questions arise relating to ecological disturbances, environmental hazards and biodiversity issues...
February 1, 2017: Current Drug Discovery Technologies
https://www.readbyqxmd.com/read/28103025/identification-of-the-first-selective-activin-receptor-like-kinase-1-inhibitor-a-reversible-version-of-l-783277
#3
Hanna Cho, Sandip Sengupta, Sean Sh Jeon, Wooyoung Hur, Hwan Geun Choi, Hong Seog Seo, Byung Joo Lee, Jeong Hun Kim, Minhwan Chung, Noo Li Jeon, Nam Doo Kim, Taebo Sim
We synthesized 1 (San78-130), a reversible version of L-783277, as a selective and potent ALK1 inhibitor. Our study showed that 1 possesses great kinase selectivity against a panel of 342 kinases and more potent activity against ALK1 than L-783277. Among the six ALK isotypes (ALK1-6), ALK1 is most significantly inhibited by compound 1. Compound 1 suppresses the BMP9-induced Smad1/5 pathway by mainly inhibiting ALK1 in C2C12 cells. Our molecular dynamics simulations suggest that H-bonding interaction between the C-4' hydroxyl group of 1 and Arg334 of ALK1 substantially contributes to the ALK1 inhibition...
January 19, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28100664/rab1-interacts-with-golph3-and-controls-golgi-structure-and-contractile-ring-constriction-during-cytokinesis-in-drosophila-melanogaster
#4
Stefano Sechi, Anna Frappaolo, Roberta Fraschini, Luisa Capalbo, Marco Gottardo, Giorgio Belloni, David M Glover, Alan Wainman, Maria Grazia Giansanti
Cytokinesis requires a tight coordination between actomyosin ring constriction and new membrane addition along the ingressing cleavage furrow. However, the molecular mechanisms underlying vesicle trafficking to the equatorial site and how this process is coupled with the dynamics of the contractile apparatus are poorly defined. Here we provide evidence for the requirement of Rab1 during cleavage furrow ingression in cytokinesis. We demonstrate that the gene omelette (omt) encodes the Drosophila orthologue of human Rab1 and is required for successful cytokinesis in both mitotic and meiotic dividing cells of Drosophila melanogaster We show that Rab1 protein colocalizes with the conserved oligomeric Golgi (COG) complex Cog7 subunit and the phosphatidylinositol 4-phosphate effector GOLPH3 at the Golgi stacks...
January 2017: Open Biology
https://www.readbyqxmd.com/read/28072516/cobalt-based-single-ion-magnets-on-an-apatite-lattice-toward-patterned-arrays-for-magnetic-memories
#5
Pavel E Kazin, Mikhail A Zykin, Walter Schnelle, Yan V Zubavichus, Konstantin A Babeshkin, Victor A Tafeenko, Claudia Felser, Martin Jansen
Single-ion magnets (SIMs) that can maintain magnetization direction on an individual transition metal atom represent the smallest atomic-scale units for future magnetic data storage devices and molecular electronics. Here we present a robust extended inorganic solid hosting efficient SIM centers, as an alternative to molecular SIM crystals. We show that unique dioxocobaltate(II) ions, confined in the channels of strontium hydroxyapatite, exhibit classical SIM features with a large energy barrier for magnetization reversal (Ueff) of 51-59 cm(-1)...
January 10, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28068317/cryogenic-optical-localization-provides-3d-protein-structure-data-with-angstrom-resolution
#6
Siegfried Weisenburger, Daniel Boening, Benjamin Schomburg, Karin Giller, Stefan Becker, Christian Griesinger, Vahid Sandoghdar
We introduce Cryogenic Optical Localization in 3D (COLD), a method to localize multiple fluorescent sites within a single small protein with Angstrom resolution. We demonstrate COLD by determining the conformational state of the cytosolic Per-ARNT-Sim domain from the histidine kinase CitA of Geobacillus thermodenitrificans and resolving the four biotin sites of streptavidin. COLD provides quantitative 3D information about small- to medium-sized biomolecules on the Angstrom scale and complements other techniques in structural biology...
February 2017: Nature Methods
https://www.readbyqxmd.com/read/28059382/improving-the-performance-of-an-electrowetting-lenticular-lens-array-by-using-a-thin-polycarbonate-chamber
#7
Junsik Lee, Junoh Kim, Cheoljoong Kim, Dooseub Shin, Gyohyun Koo, Jee Hoon Sim, Yong Hyub Won
In this paper, we used a thin polycarbonate (PC) chamber to improve the performance of an electrowetting lenticular lens array. The polycarbonate chamber changed the radius of curvature (ROC) of the oil acting as a lens, which increased the dioptric power of the liquid lens to 1666.7D. The increase in dioptric power required a reduction in the distance between the optical center of the lens and the display pixels under the chamber, which was accomplished by reducing the thickness of the chamber. The optimal thickness of the chamber was determined to be 0...
December 26, 2016: Optics Express
https://www.readbyqxmd.com/read/28057763/the-ultrastructural-organization-of-actin-and-myosin-ii-filaments-in-the-contractile-ring-new-support-for-an-old-model-of-cytokinesis
#8
John H Henson, Casey E Ditzler, Aphnie Germain, Patrick M Irwin, Eric T Vogt, Shucheng Yang, Xufeng Wu, Charles B Shuster
Despite recent advances in our understanding of the components and spatial regulation of the contractile ring (CR), the precise ultrastructure of actin and myosin II within the animal cell CR remains an unanswered question. We employed super-resolution light microscopy and platinum replica transmission electron microscopy (TEM) to determine the structural organization of actin and myosin II in isolated cortical cytoskeletons prepared from dividing sea urchin embryos. 3D structured illumination microscopy (SIM) indicated that within the CR, actin and myosin II filaments were organized into tightly packed linear arrays oriented along the axis of constriction, and restricted to a narrow zone within the furrow...
January 5, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28047328/mo-fg-campus-jep3-05-evaluation-of-4d-ct-on-rails-target-localization-methods-for-free-breathing-liver-stereotactic-body-radiotherapy-sbrt
#9
J Fan, T Lin, L Jin, L Chen, I Veltchev, L Wang, A Eldib, O Chibani, B Wang, Q Xu, R Price, C Ma
PURPOSE: Liver SBRT patients unable to tolerate breath-hold for radiotherapy are treated free-breathing with image guidance. Target localization using 3D CBCT requires extra margins to accommodate the respiratory motion. The purpose of this study is to evaluate the accuracy and reproducibility of 4D CT-on-rails in target localization for free-breathing liver SBRT. METHODS: A Siemens SOMATOM CT-on-Rails 4D with Anzai Pressure Belt system was used both as the simulation and the localization CT...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/27996096/super-resolution-structure-of-dna-significantly-differs-in-buccal-cells-of-controls-and-alzheimer-s-patients
#10
Angeles Garcia, David Huang, Amanda Righolt, Christiaan Righolt, Maria Carmela Kalaw, Shubha Mathur, Elizabeth McAvoy, James Anderson, Angela Luedke, Justine Itorralba, Sabine Mai
The advent of super-resolution microscopy allowed for new insights into cellular and physiological processes of normal and diseased cells. In this study, we report for the first time on the super-resolved DNA structure of buccal cells from patients with Alzheimer's disease (AD) vs. age- and gender-matched healthy, non-caregiver controls. In this super-resolution study cohort of 74 participants, buccal cells were collected and their spatial DNA organization in the nucleus examined by 3D Structured Illumination Microscopy (3D-SIM)...
December 20, 2016: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/27929156/correlation-of-annealing-time-with-crystal-structure-composition-and-electronic-properties-of-ch3nh3pbi3-xclx-mixed-halide-perovskite-films
#11
Maryline Ralaiarisoa, Yan Busby, Johannes Frisch, Ingo Salzmann, Jean-Jacques Pireaux, Norbert Koch
Using 3D imaging with time-of-flight secondary ion mass spectrometry (ToF-SIMS) complemented by grazing-incidence X-ray diffraction (GIXRD), we spatially resolve changes in both the composition and structure of CH3NH3I3-xClx perovskite films on conducting polymer substrates at different annealing stages, in particular, before and after complete perovskite crystallization. The early stage of annealing is characterized by phase separation throughout the entire film into domains with perovskite and domains with a dominating chloride-rich phase...
December 21, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27898297/a-novel-pfib-sample-preparation-protocol-for-correlative-3d-x-ray-cnt-and-fib-tof-sims-tomography
#12
Agnieszka Priebe, Guillaume Audoit, Jean-Paul Barnes
We present a novel sample preparation method that allows correlative 3D X-ray Computed Nano-Tomography (CNT) and Focused Ion Beam Time-Of-Flight Secondary Ion Mass Spectrometry (FIB-TOF-SIMS) tomography to be performed on the same sample. In addition, our invention ensures that samples stay unmodified structurally and chemically between the subsequent experiments. The main principle is based on modifying the topography of the X-ray CNT experimental setup before FIB-TOF-SIMS measurements by incorporating a square washer around the sample...
November 19, 2016: Ultramicroscopy
https://www.readbyqxmd.com/read/27873269/the-use-of-3d-telomere-fish-for-the-characterization-of-the-nuclear-architecture-in-ebv-positive-hodgkin-s-lymphoma
#13
Hans Knecht, Sabine Mai
The 3D nuclear architecture is closely related to cellular functions and chromosomes are organized in distinct territories. Quantitative 3D telomere FISH analysis (3D Q-FISH) and 3D super-resolution imaging (3D-SIM) at a resolution up to 80 nm as well as the recently developed combined quantitative 3D TRF2-telomere immune FISH technique (3D TRF2/Telo-Q-FISH) have substantially contributed to elucidate molecular pathogenic mechanisms of hematological diseases. Here we report the methods we applied to uncover major molecular steps involved in the pathogenesis of EBV-associated Hodgkin's lymphoma...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27856800/normal-testes-asymmetry-evaluated-by-apparent-diffusion-coefficient-and-magnetization-transfer-ratio
#14
Athina C Tsili, Alexandra Ntorkou, Dimitrios Giannakis, Nikolaos Sofikitis, Maria I Argyropoulou
BACKGROUND: In humans, the left testis generally hangs lower than the right and the right is larger than the left. Magnetic resonance imaging (MRI) represents an important adjuvant modality in the investigation of testicular diseases. PURPOSE: To assess if normal testes asymmetry is related to apparent diffusion coefficient (ADC) and magnetization transfer ratio (MTR). MATERIAL AND METHODS: The normal testes from 106 men were included. Testicular volume (TV) was calculated by using the ellipsoid formula: length × width × height × 0...
November 17, 2016: Acta Radiologica
https://www.readbyqxmd.com/read/27826080/super-resolution-for-everybody-an-image-processing-workflow-to-obtain-high-resolution-images-with-a-standard-confocal-microscope
#15
France Lam, Damien Cladière, Cyndélia Guillaume, Katja Wassmann, Susanne Bolte
In the presented work we aimed at improving confocal imaging to obtain highest possible resolution in thick biological samples, such as the mouse oocyte. We therefore developed an image processing workflow that allows improving the lateral and axial resolution of a standard confocal microscope. Our workflow comprises refractive index matching, the optimization of microscope hardware parameters and image restoration by deconvolution. We compare two different deconvolution algorithms, evaluate the necessity of denoising and establish the optimal image restoration procedure...
November 5, 2016: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/27794119/nanometer-scale-chemistry-of-a-calcite-biomineralization-template-implications-for-skeletal-composition-and-nucleation
#16
Oscar Branson, Elisa A Bonnin, Daniel E Perea, Howard J Spero, Zihua Zhu, Maria Winters, Bärbel Hönisch, Ann D Russell, Jennifer S Fehrenbacher, Alexander C Gagnon
Plankton, corals, and other organisms produce calcium carbonate skeletons that are integral to their survival, form a key component of the global carbon cycle, and record an archive of past oceanographic conditions in their geochemistry. A key aspect of the formation of these biominerals is the interaction between organic templating structures and mineral precipitation processes. Laboratory-based studies have shown that these atomic-scale processes can profoundly influence the architecture and composition of minerals, but their importance in calcifying organisms is poorly understood because it is difficult to measure the chemistry of in vivo biomineral interfaces at spatially relevant scales...
November 15, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27768294/understanding-the-magnetic-anisotropy-toward-single-ion-magnets
#17
Yin-Shan Meng, Shang-Da Jiang, Bing-Wu Wang, Song Gao
Single-molecule magnets (SMMs) can retain their magnetization status preferentially after removal of the magnetic field below a certain temperature. The unique property, magnetic bistable status, enables the molecule-scale SMM to become the next-generation high-density information storage medium. SMMs' new applications are also involved in high-speed quantum computation and molecular spintronics. The development of coordination chemistry, especially in transition metal (3d) and lanthanide (4f) complexes, diversifies SMMs by introducing new ones...
November 15, 2016: Accounts of Chemical Research
https://www.readbyqxmd.com/read/27766219/osteogenic-odontogenic-bioengineering-with-co-administration-of-simvastatin-and-hydroxyapatite-on-poly-caprolactone-based-nanofibrous-scaffold
#18
Mohammad Samiei, Marziyeh Aghazadeh, Effat Alizadeh, Naser Aslaminabadi, Soodabeh Davaran, Sajjad Shirazi, Farhad Ashrafi, Roya Salehi
Purpose: Statin is an effective factor for promoting osteogenesis. The aim of the present study was to evaluate the effect of simvastatin (SIM) and/or HA addition on changes in osteogenesis levels by human DPSCs transferred onto three-dimensional (3D) nanofibrous Poly (ε-caprolactone) (PCL)/Poly lactic acide (PLLA) polymeric scaffolds. Methods: For this purpose, a 3D nanofibrous composite scaffold of PCL/PLLA/HA was prepared by electrospinning method. SIM was added to scaffolds during DPSCs culturing step...
September 2016: Advanced Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/27753523/golgi-proteins-in-circulating-human-platelets-are-distributed-across-non-stacked-scattered-structures
#19
Shilpi Yadav, Jonathan K Williamson, Maria A Aronova, Andrew A Prince, Irina D Pokrovskaya, Richard D Leapman, Brian Storrie
Platelets are small, anucleate cell fragments that are central to hemostasis, thrombosis, and inflammation. They are derived from megakaryocytes from which they inherit their organelles. As platelets can synthesize proteins and contain many of the enzymes of the secretory pathway, one might expect all mature human platelets to contain a stacked Golgi apparatus, the central organelle of the secretory pathway. By thin section electron microscopy, stacked membranes resembling the stacked Golgi compartment in megakaryocytes and other nucleated cells can be detected in both proplatelets and platelets...
October 18, 2016: Platelets
https://www.readbyqxmd.com/read/27748959/study-of-ethanol-induced-golgi-disorganization-reveals-the-potential-mechanism-of-alcohol-impaired-n-glycosylation
#20
Carol A Casey, Ganapati Bhat, Melissa S Holzapfel, Armen Petrosyan
BACKGROUND: It is known that ethanol (EtOH) and its metabolites have a negative effect on protein glycosylation. The fragmentation of the Golgi apparatus induced by alteration of the structure of largest Golgi matrix protein, giantin, is the major consequence of damaging effects of EtOH-metabolism on the Golgi; however, the link between this and abnormal glycosylation remains unknown. Because previously we have shown that Golgi morphology dictates glycosylation, we examined the effect EtOH administration has on function of Golgi residential enzymes involved in N-glycosylation...
December 2016: Alcoholism, Clinical and Experimental Research
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